pacman::p_load(tidyverse, fishualize, patchwork, ggcorrplot)
path1 <-
'~/Git/henriquelaureano.github.io/THESIS/code/coefs/coefs1to100/'
path2 <-
'~/Git/henriquelaureano.github.io/THESIS/code/coefs/coefs101to200/'
path3 <-
'~/Git/henriquelaureano.github.io/THESIS/code/coefs/coefs201to300/'
path4 <-
'~/Git/henriquelaureano.github.io/THESIS/code/coefs/coefs301to400/'
path5 <-
'~/Git/henriquelaureano.github.io/THESIS/code/coefs/coefs401to500/'
fixednames <- c('beta1', 'beta2', 'gama1', 'gama2', 'w1', 'w2')
varnames <- c('logs2_1', 'logs2_2', 'logs2_3', 'logs2_4')
cornames <- c(
'rhoZ12', 'rhoZ13', 'rhoZ14', 'rhoZ23', 'rhoZ24', 'rhoZ34'
)
metnames <- c('conv', 'mll')
vdata <- function(data, path)
{
out <-
tibble::as_tibble(read.table(paste0(path, data)))%>%
dplyr::select(-V1)
type <- substring(data, 6, 7)
switch(type,
v1={ out <-
out%>%'colnames<-'(c(
fixednames,
varnames[1:2], cornames[1], metnames)) },
v2={ out <-
out%>%'colnames<-'(c(
fixednames,
varnames[3:4], cornames[6], metnames)) },
v3={ out <-
out%>%'colnames<-'(c(
fixednames,
varnames, cornames[c(1, 6)], metnames)) },
v4={ out <-
out%>%'colnames<-'(c(
fixednames,
varnames, cornames, metnames)) },
stop('Invalid type'))
return(out)
}
v1data <- v2data <- v3data <- v4data <- vector('list', 18)
label <- numeric(18)
l <- 1
for (i in 1:3)
{
for (j in 1:2)
{
for (k in 1:3)
{
label[l] <- paste0('cs', i, '_', j, '_', k)
v1data[[l]] <-
dplyr::bind_rows(
vdata(paste0('coefsv1_', label[l], '.txt'),
path1),
vdata(paste0('coefsv1_', label[l], '.txt'),
path2),
vdata(paste0('coefsv1_', label[l], '.txt'),
path3),
vdata(paste0('coefsv1_', label[l], '.txt'),
path4),
vdata(paste0('coefsv1_', label[l], '.txt'),
path5)
)
v2data[[l]] <-
dplyr::bind_rows(
vdata(paste0('coefsv2_', label[l], '.txt'),
path1),
vdata(paste0('coefsv2_', label[l], '.txt'),
path2),
vdata(paste0('coefsv2_', label[l], '.txt'),
path3),
vdata(paste0('coefsv2_', label[l], '.txt'),
path4),
vdata(paste0('coefsv2_', label[l], '.txt'),
path5)
)
v3data[[l]] <-
dplyr::bind_rows(
vdata(paste0('coefsv3_', label[l], '.txt'),
path1),
vdata(paste0('coefsv3_', label[l], '.txt'),
path2),
vdata(paste0('coefsv3_', label[l], '.txt'),
path3),
vdata(paste0('coefsv3_', label[l], '.txt'),
path4),
vdata(paste0('coefsv3_', label[l], '.txt'),
path5)
)
v4data[[l]] <-
dplyr::bind_rows(
vdata(paste0('coefsv4_', label[l], '.txt'),
path1),
vdata(paste0('coefsv4_', label[l], '.txt'),
path2),
vdata(paste0('coefsv4_', label[l], '.txt'),
path3),
vdata(paste0('coefsv4_', label[l], '.txt'),
path4),
vdata(paste0('coefsv4_', label[l], '.txt'),
path5)
)
l <- l+1
}
}
}
## str(v1data);length(v1data)
## summary(v2data[9][[1]]$beta1)
## plot(seq(453), v2data[9][[1]]$beta1)
## str(v2data[9][[1]])
v2data[9][[1]] <- v2data[9][[1]][-437, ]
## str(v2data);length(v2data)
## summary(v3data[10][[1]]$gama1)
## plot(seq(496), v3data[10][[1]]$gama1)
## str(v3data[10][[1]])
v3data[10][[1]] <- v3data[10][[1]][-329, ]
## str(v3data);length(v3data)
## str(v4data);length(v4data)
cif1 <- setNames(c( 3, 2.6, 2.5, 4, 5, 10), fixednames)
cif2 <- setNames(c(-2, -1.5, 1, 1.5, 3, 4), fixednames)
logvars <- setNames(log(c(1, 0.6, 0.7, 0.9)), varnames)
rhoZs <- setNames(atanh(c(0.1, -0.5, 0.3, 0.3, -0.4, 0.2)), cornames)
vtrue <- function(data.cif1, data.cif2)
{
out <- rep(c(replicate(data.cif1, n=3, simplify=FALSE),
replicate(data.cif2, n=3, simplify=FALSE)), 3)
return(out)
}
v1cif1 <- c(cif1, logvars[1:2], rhoZs[1])
v1cif2 <- c(cif2, logvars[1:2], rhoZs[1])
v1true <- vtrue(v1cif1, v1cif2)
v2cif1 <- c(cif1, logvars[3:4], rhoZs[6])
v2cif2 <- c(cif2, logvars[3:4], rhoZs[6])
v2true <- vtrue(v2cif1, v2cif2)
v3cif1 <- c(cif1, logvars, rhoZs[c(1, 6)])
v3cif2 <- c(cif2, logvars, rhoZs[c(1, 6)])
v3true <- vtrue(v3cif1, v3cif2)
v4cif1 <- c(cif1, logvars, rhoZs)
v4cif2 <- c(cif2, logvars, rhoZs)
v4true <- vtrue(v4cif1, v4cif2)
BIAS QUANTILE
cerror <- function(data, true, data_label) {
coefs <- data%>%dplyr::select(-c(conv, mll))
error <- coefs
for (i in seq(ncol(coefs))) { error[i] <- true[i]-coefs[i] }
out <- error%>%
dplyr::summarize_all(mean)%>%
dplyr::add_row(
error%>%
dplyr::summarize_all(quantile, c(0.025, 0.975)))%>%
dplyr::add_row(
error%>%
dplyr::summarize_all(sd))%>%
dplyr::mutate(label=c('mean', 'q025', 'q975', 'sd'),
conv=1-mean(data$conv),
nr=nrow(data),
data=data_label)
return(out)
}
label <- sub('cs1_', 'cs02-', label)
label <- sub('cs2_', 'cs05-', label)
label <- sub('cs3_', 'cs10-', label)
label <- sub('1_', 'high-', label)
label <- sub('2_', '-low-', label)
label <- sub('-1$', '-05k', label)
label <- sub('-2$', '-30k', label)
label <- sub('-3$', '-60k', label)
v1error <- v2error <- v3error <- v4error <- NULL
for (i in seq(18))
{
v1error <-
v1error%>%
dplyr::bind_rows(cerror(v1data[[i]], v1true[[i]], label[i]))
v2error <-
v2error%>%
dplyr::bind_rows(cerror(v2data[[i]], v2true[[i]], label[i]))
v3error <-
v3error%>%
dplyr::bind_rows(cerror(v3data[[i]], v3true[[i]], label[i]))
v4error <-
v4error%>%
dplyr::bind_rows(cerror(v4data[[i]], v4true[[i]], label[i]))
}
## v1error
## v2error
## v3error
## v4error
inside <- function(par, errordata)
{
out <-
errordata%>%
dplyr::select(par, label, conv, nr, data)%>%
tidyr::pivot_wider(names_from=label, values_from=par)
out$data <-
forcats::fct_relevel(forcats::as_factor(out$data), rev)
return(out)
}
biasformat <- function(par, errordatas)
{
out <- dplyr::bind_rows(inside(par, errordatas[[1]]),
inside(par, errordatas[[2]]),
inside(par, errordatas[[3]]),
inside(par, errordatas[[4]]),
.id='v')
out$v <- forcats::fct_recode(out$v,
'RISK MODEL' ='1',
'TIME MODEL' ='2',
'BLOCK-DIAG MODEL'='3',
'COMPLETE MODEL' ='4')
return(out)
}
bias2plot <- function(df, title)
{
ggplot(df, aes(ymin=q025, ymax=q975, x=data, size=nr))+
geom_linerange(position=position_dodge(width=0.2), color='#8A8D8F')+
## geom_linerange(position=position_dodge(width=0.2), color='#0096c8')+
## geom_linerange(position=position_dodge(width=0.2), color='#262626')+
geom_point(mapping=aes(x=data, y=mean), size=3,
shape=21, color='black', fill='white', stroke=2)+
facet_grid(~v, scales='free_x')+
geom_hline(yintercept=0, linetype='dashed')+
labs(x=NULL, y='Bias',
title=title,
subtitle='with 2.5% and 97.5% quantiles',
size='Fittings')+
coord_flip()+
## theme_minimal()+
theme(
strip.background=element_rect(colour='black', fill='white'),
legend.box.background=element_rect(color='black'),
legend.position='bottom',
plot.title=element_text(size=16),
plot.subtitle=element_text(size=15, face='italic'),
axis.text.x=element_text(size=13),
axis.text.y=element_text(size=14),
axis.title.x=element_text(size=14,
margin=unit(c(t=3, r=0, b=0, l=0),
'mm')),
## legend.justification=c(1, 0),
legend.title=element_text(size=14),
legend.text=element_text(size=13),
strip.text.x=element_text(size=14, face='bold')
)
}
bias <- function(par, title)
{
out <- biasformat(
par,
list(v1error, v2error, v3error, v4error)
)
bias2plot(out, title=title)
}
bias('beta1', expression(bold('Parameter:'~beta[1])))
bias('beta2', expression(bold('Parameter:'~beta[2])))
bias('gama1', expression(bold('Parameter:'~gamma[1])))
bias('gama2', expression(bold('Parameter:'~gamma[2])))
bias('w1', expression(bold('Parameter:'~w[1])))
bias('w2', expression(bold('Parameter:'~w[2])))
par <- 'logs2_1'
out <- dplyr::bind_rows(inside(par, v1error),
inside(par, v3error),
inside(par, v4error),
.id='v')
out$v <- forcats::fct_recode(out$v,
'RISK MODEL' ='1',
'BLOCK-DIAG MODEL'='2',
'COMPLETE MODEL' ='3')
bias2plot(out, expression(bold('Parameter:'~log(sigma[1]^2))))
par <- 'logs2_2'
out <- dplyr::bind_rows(inside(par, v1error),
inside(par, v3error),
inside(par, v4error),
.id='v')
out$v <- forcats::fct_recode(out$v,
'RISK MODEL' ='1',
'BLOCK-DIAG MODEL'='2',
'COMPLETE MODEL' ='3')
bias2plot(out, expression(bold('Parameter:'~log(sigma[2]^2))))
par <- 'logs2_3'
out <- dplyr::bind_rows(inside(par, v2error),
inside(par, v3error),
inside(par, v4error),
.id='v')
out$v <- forcats::fct_recode(out$v,
'TIME MODEL' ='1',
'BLOCK-DIAG MODEL'='2',
'COMPLETE MODEL' ='3')
bias2plot(out, expression(bold('Parameter:'~log(sigma[3]^2))))
par <- 'logs2_4'
out <- dplyr::bind_rows(inside(par, v2error),
inside(par, v3error),
inside(par, v4error),
.id='v')
out$v <- forcats::fct_recode(out$v,
'TIME MODEL' ='1',
'BLOCK-DIAG MODEL'='2',
'COMPLETE MODEL' ='3')
bias2plot(out, expression(bold('Parameter:'~log(sigma[4]^2))))
par <- 'rhoZ12'
out <- dplyr::bind_rows(inside(par, v1error),
inside(par, v3error),
inside(par, v4error),
.id='v')
out$v <- forcats::fct_recode(out$v,
'RISK MODEL' ='1',
'BLOCK-DIAG MODEL'='2',
'COMPLETE MODEL' ='3')
bias2plot(out, expression(bold('Parameter:'~z(rho[12]))))
par <- 'rhoZ34'
out <- dplyr::bind_rows(inside(par, v2error),
inside(par, v3error),
inside(par, v4error),
.id='v')
out$v <- forcats::fct_recode(out$v,
'TIME MODEL' ='1',
'BLOCK-DIAG MODEL'='2',
'COMPLETE MODEL' ='3')
bias2plot(out, expression(bold('Parameter:'~z(rho[34]))))
bias2plot_rho <- function(df, title)
{
ggplot(df, aes(ymin=q025, ymax=q975, x=data, size=nr))+
geom_linerange(position=position_dodge(width=0.2), color='#8A8D8F')+
geom_point(mapping=aes(x=data, y=mean), size=3,
shape=21, color='black', fill='white', stroke=2)+
facet_grid(~v, scales='free_x', labeller=label_parsed)+
geom_hline(yintercept=0, linetype='dashed')+
labs(x=NULL, y='Bias',
title=title,
subtitle='with 2.5% and 97.5% quantiles',
size='Fittings')+
coord_flip()+
## theme_minimal()+
theme(
strip.background=element_rect(colour='black', fill='white'),
legend.box.background=element_rect(color='black'),
legend.position='bottom',
plot.title=element_text(size=16),
plot.subtitle=element_text(size=15, face='italic'),
axis.text.x=element_text(size=13),
axis.text.y=element_text(size=14),
axis.title.x=element_text(size=14,
margin=unit(c(t=3, r=0, b=0, l=0),
'mm')),
## legend.justification=c(1, 0),
legend.title=element_text(size=14),
legend.text=element_text(size=13),
strip.text.x=element_text(size=14)
)+
guides(size=guide_legend(nrow=1))
}
out <- dplyr::bind_rows(inside('rhoZ13', v4error),
inside('rhoZ24', v4error),
inside('rhoZ14', v4error),
inside('rhoZ23', v4error),
.id='v')
out$v <- forcats::fct_recode(out$v,
'bold(z(rho[13]))'='1',
'bold(z(rho[24]))'='2',
'bold(z(rho[14]))'='3',
'bold(z(rho[23]))'='4')
bias2plot_rho(out,
expression(bold("Complete model's cross-correlations")))
BIAS SD
bias2plot2 <- function(df, title)
{
ggplot(df, aes(ymin=mean-1.96*sd, ymax=mean+1.96*sd, x=data, size=nr))+
geom_linerange(position=position_dodge(width=0.2), color='#8A8d8f')+
geom_point(mapping=aes(x=data, y=mean), size=3,
shape=21, color='black', fill='white', stroke=2)+
facet_grid(~v, scales='free_x')+
geom_hline(yintercept=0, linetype='dashed')+
labs(x=NULL, y='Bias',
title=title,
subtitle='with \u00b1 1.96 standard deviations',
size='Fittings')+
coord_flip()+
## theme_minimal()+
theme(
strip.background=element_rect(colour='black', fill='white'),
legend.box.background=element_rect(color='black'),
legend.position='bottom',
plot.title=element_text(size=16),
plot.subtitle=element_text(size=15, face='italic'),
axis.text.x=element_text(size=13),
axis.text.y=element_text(size=14),
axis.title.x=element_text(size=14,
margin=unit(c(t=3, r=0, b=0, l=0),
'mm')),
## legend.justification=c(1, 0),
legend.title=element_text(size=14),
legend.text=element_text(size=13),
strip.text.x=element_text(size=14, face='bold')
)
}
bias2 <- function(par, title)
{
out <- biasformat(
par,
list(v1error, v2error, v3error, v4error)
)
bias2plot2(out, title=title)
}
bias2('beta1', expression(bold('Parameter:'~beta[1])))
bias2('beta2', expression(bold('Parameter:'~beta[2])))
bias2('gama1', expression(bold('Parameter:'~gamma[1])))
bias2('gama2', expression(bold('Parameter:'~gamma[2])))
bias2('w1', expression(bold('Parameter:'~w[1])))
bias2('w2', expression(bold('Parameter:'~w[2])))
par <- 'logs2_1'
out <- dplyr::bind_rows(inside(par, v1error),
inside(par, v3error),
inside(par, v4error),
.id='v')
out$v <- forcats::fct_recode(out$v,
'RISK MODEL' ='1',
'BLOCK-DIAG MODEL'='2',
'COMPLETE MODEL' ='3')
bias2plot2(out, expression(bold('Parameter:'~log(sigma[1]^2))))
par <- 'logs2_2'
out <- dplyr::bind_rows(inside(par, v1error),
inside(par, v3error),
inside(par, v4error),
.id='v')
out$v <- forcats::fct_recode(out$v,
'RISK MODEL' ='1',
'BLOCK-DIAG MODEL'='2',
'COMPLETE MODEL' ='3')
bias2plot2(out, expression(bold('Parameter:'~log(sigma[2]^2))))
par <- 'logs2_3'
out <- dplyr::bind_rows(inside(par, v2error),
inside(par, v3error),
inside(par, v4error),
.id='v')
out$v <- forcats::fct_recode(out$v,
'TIME MODEL' ='1',
'BLOCK-DIAG MODEL'='2',
'COMPLETE MODEL' ='3')
bias2plot2(out, expression(bold('Parameter:'~log(sigma[3]^2))))
par <- 'logs2_4'
out <- dplyr::bind_rows(inside(par, v2error),
inside(par, v3error),
inside(par, v4error),
.id='v')
out$v <- forcats::fct_recode(out$v,
'TIME MODEL' ='1',
'BLOCK-DIAG MODEL'='2',
'COMPLETE MODEL' ='3')
bias2plot2(out, expression(bold('Parameter:'~log(sigma[4]^2))))
par <- 'rhoZ12'
out <- dplyr::bind_rows(inside(par, v1error),
inside(par, v3error),
inside(par, v4error),
.id='v')
out$v <- forcats::fct_recode(out$v,
'RISK MODEL' ='1',
'BLOCK-DIAG MODEL'='2',
'COMPLETE MODEL' ='3')
bias2plot2(out, expression(bold('Parameter:'~z(rho[12]))))
par <- 'rhoZ34'
out <- dplyr::bind_rows(inside(par, v2error),
inside(par, v3error),
inside(par, v4error),
.id='v')
out$v <- forcats::fct_recode(out$v,
'TIME MODEL' ='1',
'BLOCK-DIAG MODEL'='2',
'COMPLETE MODEL' ='3')
bias2plot2(out, expression(bold('Parameter:'~z(rho[34]))))
bias2plot2_rho <- function(df, title)
{
ggplot(df, aes(ymin=mean-1.96*sd, ymax=mean+1.96*sd, x=data, size=nr))+
geom_linerange(position=position_dodge(width=0.2), color='8A8d8f')+
geom_point(mapping=aes(x=data, y=mean), size=3,
shape=21, color='black', fill='white', stroke=2)+
facet_grid(~v, scales='free_x', labeller=label_parsed)+
geom_hline(yintercept=0, linetype='dashed')+
labs(x=NULL, y='Bias',
title=title,
subtitle='with \u00b1 1.96 standard deviations',
size='Fittings')+
coord_flip()+
## theme_minimal()+
theme(
strip.background=element_rect(colour='black', fill='white'),
legend.box.background=element_rect(color='black'),
legend.position='bottom',
plot.title=element_text(size=16),
plot.subtitle=element_text(size=15, face='italic'),
axis.text.x=element_text(size=13),
axis.text.y=element_text(size=14),
axis.title.x=element_text(size=14,
margin=unit(c(t=3, r=0, b=0, l=0),
'mm')),
## legend.justification=c(1, 0),
legend.title=element_text(size=14),
legend.text=element_text(size=13),
strip.text.x=element_text(size=14)
)+
guides(size=guide_legend(nrow=1))
}
out <- dplyr::bind_rows(inside('rhoZ13', v4error),
inside('rhoZ24', v4error),
inside('rhoZ14', v4error),
inside('rhoZ23', v4error),
.id='v')
out$v <- forcats::fct_recode(out$v,
'bold(z(rho[13]))'='1',
'bold(z(rho[24]))'='2',
'bold(z(rho[14]))'='3',
'bold(z(rho[23]))'='4')
bias2plot2_rho(out,
expression(bold("Complete model's cross-correlations")))
CIF
cmean <- function(data, data_label)
{
df <- data%>%dplyr::select(beta1, beta2, gama1, gama2, w1, w2)
out <-
df%>%
dplyr::summarize_all(mean)%>%
dplyr::mutate(data=data_label)
return(out)
}
lcmean <- function(datas, data_labels)
{
out <- NULL
for (i in seq(18))
{
out <- out%>%bind_rows(cmean(datas[[i]], data_labels[[i]]))
}
return(out)
}
df_cmean <-
dplyr::bind_rows(lcmean(v1data, label),
lcmean(v2data, label),
lcmean(v3data, label),
lcmean(v4data, label), .id='v')%>%
dplyr::mutate(v=v%>%
forcats::fct_recode('RISK MODEL' ='1',
'TIME MODEL' ='2',
'BLOCK-DIAG MODEL'='3',
'COMPLETE MODEL' ='4'))
time <- seq(30, 79.9, length.out=100)
delta <- 80
compCifs <- function(df_cmean.obj)
{
beta1 <- unlist(df_cmean.obj%>%dplyr::select(beta1))
n <- length(beta1)
beta2 <- unlist(df_cmean.obj%>%dplyr::select(beta2))
gama1 <- unlist(df_cmean.obj%>%dplyr::select(gama1))
gama2 <- unlist(df_cmean.obj%>%dplyr::select(gama2))
w1 <- unlist(df_cmean.obj%>%dplyr::select(w1))
w2 <- unlist(df_cmean.obj%>%dplyr::select(w2))
cif1 <- vector(mode='list', length=n)
cif2 <- vector(mode='list', length=n)
for (i in seq(n))
{
risk1 <- exp(beta1[i])
risk2 <- exp(beta2[i])
level <- 1+risk1+risk2
gt <- atanh(2*time/delta-1)
traje1 <- pnorm(w1[i]*gt-gama1[i])
traje2 <- pnorm(w2[i]*gt-gama2[i])
cif1[[i]] <- risk1/level*traje1
cif2[[i]] <- risk2/level*traje2
}
return(list(cif1=cif1, cif2=cif2))
}
cifsHigh <- compCifs(dplyr::filter(df_cmean, grepl('high', data)))
cifsLow <- compCifs(dplyr::filter(df_cmean, grepl( 'low', data)))
getCIF <- function(compCifs.obj, n)
{
cif1 <- cif2 <- NULL
for (i in seq(n))
{
cif1 <- c(cif1, unlist(compCifs.obj[['cif1']][i]))
cif2 <- c(cif2, unlist(compCifs.obj[['cif2']][i]))
}
return(cbind(cif1, cif2))
}
cifs_high <- getCIF(cifsHigh, 36)
cifs_low <- getCIF(cifsLow, 36)
times <- rep(time, 36)
model <- rep(c('RISK MODEL',
'TIME MODEL',
'BLOCK-DIAG MODEL',
'COMPLETE MODEL'), each=900)
labels <- unique(sub('-high|--low', '', label))
labels <- rep(rep(labels, each=100), 4)
dfcif_type <- function(data)
{
out <- tibble::tibble(cif =data,
time =times,
model=forcats::as_factor(model),
label=labels)
return(out)
}
dfcif1_high <- dfcif_type(cifs_high[, 'cif1'])
dfcif2_high <- dfcif_type(cifs_high[, 'cif2'])
dfcif1_low <- dfcif_type(cifs_low[, 'cif1'])
dfcif2_low <- dfcif_type(cifs_low[, 'cif2'])
cif2plot <- function(dfcif_type, descr)
{
ggplot(dfcif_type, aes(x=time, y=cif, color=label))+
geom_line(size=1.5)+
facet_grid(~model)+
theme_minimal()+
labs(x='Time', y=NULL, color=NULL,
title=descr, subtitle='True curve in dashed black')+
## scale_color_fish_d(option='Scarus_quoyi')+
scale_color_brewer(palette='Spectral')+
theme(
axis.text.x=element_text(size=13),
axis.text.y=element_text(size=13),
## legend.position=c(0.05, 0.65),
legend.position='top',
legend.text=element_text(size=14),
legend.box.background=element_rect(color='black'),
strip.background=element_rect(colour='black', fill='white'),
strip.text.x=element_text(size=14, face='bold'),
plot.title=element_text(size=15, face='bold'),
plot.subtitle=element_text(size=15, face='italic'),
axis.title.x=element_text(size=14,
margin=unit(c(t=3, r=0, b=0, l=0),
'mm'))
)+
guides(color=guide_legend(nrow=3))
}
truefixed <-
tibble::tribble(
~beta1, ~beta2, ~gama1, ~gama2, ~w1, ~w2,
3, 2.6, 2.5, 4, 5, 10,
-2, -1.5, 1, 1.5, 3, 4,
)
ciftrue_high <- compCifs(truefixed[1, ])
ciftrue_low <- compCifs(truefixed[2, ])
ciftrue <- function(data)
{
out <- tibble::tibble(time=time, cif=unlist(data))
return(out)
}
cif1true_high <- ciftrue(ciftrue_high[['cif1']])
cif2true_high <- ciftrue(ciftrue_high[['cif2']])
cif1true_low <- ciftrue(ciftrue_low[['cif1']])
cif2true_low <- ciftrue(ciftrue_low[['cif2']])
p1 <-
cif2plot(dfcif1_high, descr='CIF of failure cause 1')+
geom_line(cif1true_high, mapping=aes(x=time, y=cif),
color='black', size=1.5, linetype='dashed')
p2 <-
cif2plot(dfcif2_high, descr='CIF of failure cause 2')+
geom_line(cif2true_high, mapping=aes(x=time, y=cif),
color='black', size=1.5, linetype='dashed')+
theme(legend.position='none')
p1/p2+plot_annotation(title='HIGH CIF SCENARIO',
theme=theme(plot.title=element_text(face='bold')))
p3 <-
cif2plot(dfcif1_low, descr='CIF of failure cause 1')+
geom_line(cif1true_low, mapping=aes(x=time, y=cif),
color='black', size=1.5, linetype='dashed')
p4 <-
cif2plot(dfcif2_low, descr='CIF of failure cause 2')+
geom_line(cif2true_low, mapping=aes(x=time, y=cif),
color='black', size=1.5, linetype='dashed')+
theme(legend.position='none')
p3/p4+plot_annotation(title='LOW CIF SCENARIO',
theme=theme(plot.title=element_text(face='bold')))
p5 <-
p1+
theme(legend.position='right',
strip.text.x=element_text(size=13.25, face='bold'))+
guides(color=guide_legend(ncol=1))
p6 <-
p2+
theme(strip.text.x=element_text(size=13.25, face='bold'))
p7 <-
p3+
theme(legend.position='right',
strip.text.x=element_text(size=13.25, face='bold'))+
guides(color=guide_legend(ncol=1))
p8 <-
p4+
theme(strip.text.x=element_text(size=13.25, face='bold'))
p5/p6
p7/p8
HISTO LOGS2
data.label <- function(data, label)
{
out <- data%>%dplyr::mutate(scenario=label)
return(out)
}
logs2pilha <- function(data1, data2, data3, par, label)
{
out1 <- out2 <- out3 <- NULL
for (i in seq(18))
{
out1 <-
out1%>%
dplyr::bind_rows(data.label(data1[[i]]%>%dplyr::select(par),
label[[i]]))
out2 <-
out2%>%
dplyr::bind_rows(data.label(data2[[i]]%>%dplyr::select(par),
label[[i]]))
out3 <-
out3%>%
dplyr::bind_rows(data.label(data3[[i]]%>%dplyr::select(par),
label[[i]]))
}
out <-
dplyr::bind_rows(out1, out2, out3, .id='v')%>%
dplyr::filter(scenario == 'cs02-high-60k' |
scenario == 'cs05-high-60k' |
scenario == 'cs10-high-60k')
return(out)
}
histo <- function(data, true, title)
{
ggplot(data, aes(x=par, color=scenario))+
## geom_density(alpha=0.6)+
geom_density(size=1)+
facet_wrap(~v, scales='free')+
## scale_fill_brewer(palette='Spectral')+
## scale_fill_viridis_d()+
scale_color_fish_d(option='Trimma_lantana')+
geom_vline(xintercept=true, linetype='dashed', size=1)+
labs(x=NULL, y=NULL, color=NULL,
title=title, subtitle='True value in dashed black')+
theme_minimal()+
theme(
legend.position='bottom',
legend.box.background=element_rect(color='black'),
legend.text=element_text(size=14),
plot.title=element_text(size=15),
plot.subtitle=element_text(size=13, face='italic'),
strip.background=element_rect(color='black', fill='white'),
strip.text.x=element_text(size=13, face='bold'),
axis.text.x=element_text(size=12),
axis.text.y=element_text(size=12)
)
}
logs2_1df <-
logs2pilha(v1data, v3data, v4data, 'logs2_1', label)%>%
dplyr::rename(par=logs2_1)%>%
dplyr::mutate(v=v%>%
forcats::fct_recode('RISK MODEL' ='1',
'BLOCK-DIAG MODEL'='2',
'COMPLETE MODEL' ='3'))
logs2_2df <-
logs2pilha(v1data, v3data, v4data, 'logs2_2', label)%>%
dplyr::rename(par=logs2_2)%>%
dplyr::mutate(v=v%>%
forcats::fct_recode('RISK MODEL' ='1',
'BLOCK-DIAG MODEL'='2',
'COMPLETE MODEL' ='3'))
logs2_3df <-
logs2pilha(v2data, v3data, v4data, 'logs2_3', label)%>%
dplyr::rename(par=logs2_3)%>%
dplyr::mutate(v=v%>%
forcats::fct_recode('TIME MODEL' ='1',
'BLOCK-DIAG MODEL'='2',
'COMPLETE MODEL' ='3'))
logs2_4df <-
logs2pilha(v2data, v3data, v4data, 'logs2_4', label)%>%
dplyr::rename(par=logs2_4)%>%
dplyr::mutate(v=v%>%
forcats::fct_recode('TIME MODEL' ='1',
'BLOCK-DIAG MODEL'='2',
'COMPLETE MODEL' ='3'))
p1 <-
histo(logs2_1df, log(1),
expression(bold('Parameter:'~log(sigma[1]^2))))+
theme(legend.position='none')
p2 <-
histo(logs2_2df, log(0.6),
expression(bold('Parameter:'~log(sigma[2]^2))))+
theme(legend.position='none')
p3 <-
histo(logs2_3df, log(0.7),
expression(bold('Parameter:'~log(sigma[3]^2))))+
theme(legend.position='none')
p4 <-
histo(logs2_4df, log(0.9),
expression(bold('Parameter:'~log(sigma[4]^2))))
p1/p2/p3/p4
HISTO RHOZ
crossco <- function()
{
out <- NULL
for (i in seq(18))
{
out <-
out%>%
dplyr::bind_rows(data.label(
v4data[[i]]%>%
dplyr::select(rhoZ13, rhoZ24, rhoZ14, rhoZ23),
label[[i]]
))
}
out <- out%>%
tidyr::pivot_longer(
!scenario, names_to='par', values_to='value'
)%>%
dplyr::mutate(par=forcats::as_factor(par)%>%
forcats::fct_recode(
'bold(z(rho[13]))'='rhoZ13',
'bold(z(rho[24]))'='rhoZ24',
'bold(z(rho[14]))'='rhoZ14',
'bold(z(rho[23]))'='rhoZ23'))%>%
dplyr::filter(scenario == 'cs02-high-60k' |
scenario == 'cs05-high-60k' |
scenario == 'cs10-high-60k')
return(out)
}
rhoZ_df <- crossco()
rhoZtrue <-
tibble::tibble(
par=forcats::as_factor(levels(rhoZ_df$par)),
value=atanh(c(-0.5, -0.4, 0.3, 0.3))
)
rhoZ12_df <-
logs2pilha(v1data, v3data, v4data, 'rhoZ12', label)%>%
dplyr::rename(par=rhoZ12)%>%
dplyr::mutate(v=v%>%
forcats::fct_recode('RISK MODEL' ='1',
'BLOCK-DIAG MODEL'='2',
'COMPLETE MODEL' ='3'))
rhoZ34_df <-
logs2pilha(v2data, v3data, v4data, 'rhoZ34', label)%>%
dplyr::rename(par=rhoZ34)%>%
dplyr::mutate(v=v%>%
forcats::fct_recode('TIME MODEL' ='1',
'BLOCK-DIAG MODEL'='2',
'COMPLETE MODEL' ='3'))
p5 <-
histo(rhoZ12_df, atanh(0.1),
expression(bold('Parameter:'~z(rho[12]))))+
theme(legend.position='none')
p6 <-
histo(rhoZ34_df, atanh(0.2),
expression(bold('Parameter:'~z(rho[34]))))+
theme(legend.position='none')
p7 <-
ggplot(rhoZ_df, aes(x=value, color=scenario))+
geom_density(size=1)+
facet_grid(~par, scales='free', labeller=label_parsed)+
## scale_fill_brewer(palette='Spectral')+
## scale_fill_viridis_d()+
scale_color_fish_d(option='Trimma_lantana')+
geom_vline(rhoZtrue, mapping=aes(xintercept=value),
linetype='dashed', size=1)+
labs(x=NULL, y=NULL, color=NULL,
title="Complete model's cross-correlations",
subtitle='True value in dashed black')+
theme_minimal()+
theme(
legend.position='bottom',
legend.box.background=element_rect(color='black'),
legend.text=element_text(size=14),
plot.title=element_text(size=15, face='bold'),
plot.subtitle=element_text(size=13, face='italic'),
strip.background=element_rect(color='black', fill='white'),
strip.text.x=element_text(size=13, face='bold'),
axis.text.x=element_text(size=12),
axis.text.y=element_text(size=12)
)
p5/p6/p7
COR
thepilha <- function()
{
out <- NULL
for (i in seq(18))
{
out <-
out%>%
dplyr::bind_rows(data.label(v4data[[i]]%>%
dplyr::select(-c(conv, mll)),
label[[i]]))
}
out <-
out%>%
dplyr::filter(scenario == 'cs10-high-60k')%>%
dplyr::select(!scenario)
return(out)
}
v4pars <- thepilha()
v4cor <- round(cor(v4pars), 1)
corlabels <- c(expression(beta[1]),
expression(beta[2]),
expression(gamma[1]),
expression(gamma[2]),
expression(w[1]),
expression(w[2]),
expression(log(sigma[1]^2)),
expression(log(sigma[2]^2)),
expression(log(sigma[3]^2)),
expression(log(sigma[4]^2)),
expression(z(rho[12])),
expression(z(rho[13])),
expression(z(rho[14])),
expression(z(rho[23])),
expression(z(rho[24])),
expression(z(rho[34])))
ggcorrplot(v4cor,
type='lower',
lab=TRUE,
lab_size=6,
tl.cex=18,
title='cs10-high-60k, complete model',
legend.title=NULL,
## colors=c('#91bfdb', '#ffffbf', '#fc8d59'),
## colors=fishualize::fish(n=4, option='Trimma_lantana'),
colors=fishualize::fish(n=3, option='Trimma_lantana'),
ggtheme=theme(
plot.title=element_text(size=18, face='bold'),
axis.ticks=element_blank(),
legend.text=element_text(size=15),
panel.background=element_rect(fill='white')
))+
scale_x_discrete(labels=corlabels[-1])+
scale_y_discrete(labels=corlabels[-16])+
## scale_fill_viridis_c(option='plasma', direction=-1)
## scale_fill_distiller(palette='Greys', direction=1)+
## scale_fill_fish(option='Trimma_lantana')+
guides(fill=guide_colorbar(barheight=38.5))
